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    1.3k repositories

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•61•23•16•Updated Jan 31, 2025Jan 31, 2025

    • viral-core

      Public
      viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux
      Python
      •
      Other
      •1•4•10•2•Updated Jan 31, 2025Jan 31, 2025

    • viral-baseimage

      Public
      Broad Viral Genomics base docker image
      Shell
      •
      Other
      •1•1•1•1•Updated Jan 31, 2025Jan 31, 2025

    • ABC-Enhancer-Gene-Prediction

      Public
      Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
      Python
      •
      MIT License
      •64•212•7•1•Updated Jan 31, 2025Jan 31, 2025

    • rock-pigean

      Public
      PIGEAN-related workflows
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•7•Updated Jan 31, 2025Jan 31, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•4•1•11•Updated Jan 31, 2025Jan 31, 2025

    • stp_segmentation_wdl

      Public
      WDL
      •0•0•0•1•Updated Jan 31, 2025Jan 31, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•9•Updated Jan 30, 2025Jan 30, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•92•10•7•Updated Jan 30, 2025Jan 30, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•69•7•13•Updated Jan 30, 2025Jan 30, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•177•74•24•Updated Jan 30, 2025Jan 30, 2025

    • cellpainting-gallery

      Public
      Cell Painting Gallery
      Other
      •13•76•7•1•Updated Jan 30, 2025Jan 30, 2025

    • PANOPLY

      Public
      Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
      R
      •
      Other
      •15•33•0•1•Updated Jan 30, 2025Jan 30, 2025

    • EmmaEmb

      Public
      Python
      •
      MIT License
      •0•4•0•0•Updated Jan 30, 2025Jan 30, 2025

    • ega_submissions

      Public
      Python
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • mitograph

      Public
      Rust
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Jan 30, 2025Jan 30, 2025

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•3•Updated Jan 30, 2025Jan 30, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •597•1.8k•1.2k•137•Updated Jan 30, 2025Jan 30, 2025

    • celldega_Xenium_Prime_Mouse_Brain_Coronal_FF_outs

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•6•Updated Jan 30, 2025Jan 30, 2025

    • TAG-public

      Public
      Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)
      WDL
      •3•5•1•17•Updated Jan 30, 2025Jan 30, 2025

    • dsp-appsec-infrastructure-apps

      Public
      This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.
      application-securityappsecsecurity-scannersecure-developmentsecurity-automationsecurity-toolsdevsecopssecurity-scanappsecurityappsec-tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•0•2•Updated Jan 30, 2025Jan 30, 2025

    • malaria

      Public
      R
      •
      MIT License
      •0•1•2•0•Updated Jan 30, 2025Jan 30, 2025

    • thurloe

      Public
      A simple service to store arbitrary key/value pairs
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•5•Updated Jan 30, 2025Jan 30, 2025

    • scp-ingest-pipeline

      Public
      File Ingest Pipeline for Single Cell Portal
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•1•Updated Jan 30, 2025Jan 30, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•5•7•Updated Jan 30, 2025Jan 30, 2025

    • Bb_pangenome

      Public
      All required code and data for pangenomic analysis of Borrelia burgdorferi. Lemieux Lab 2025.
      0•1•0•0•Updated Jan 30, 2025Jan 30, 2025

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationcloudbioinformaticsscalaexecutorhpccontainerswdlga4gh
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •359•1k•744•48•Updated Jan 30, 2025Jan 30, 2025